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It turns out that I was chasing down the wrong problem. After further investigation it appears that headers are being properly constructed for custom messages based on custom messages. My problem was that one of the messages (that happened to be one of these kind of messages) was not in the CMakeLists.txt and so was not being processed by catkin_make. When make_libraries was being called, it couldn't find the appropriate catkin generated files.

Thank you for your comments and suggestions, especially @allenh1 for pointing me to the CMake file.